如何可视化基因网络和基因聚类组？

发布于 2024-09-19 02:31:31 字数 731 浏览 6 评论 0原文

我正在处理生物数据——即基因组。例如：

group 1: geneA geneB geneC
group 2: geneD geneE
group 3: geneF geneG geneH

对于每对基因，geneX 和 geneY 我有一个分数，说明这两个基因的相似程度（实际上，我有两个分数，因为我使用了 BLAST是“定向”：我首先针对所有其他基因搜索 geneX，然后针对所有其他基因搜索 geneY，所以我有两个 geneX--geneY > 分数，但我想我可以取两者中较低的分数，或者平均值）。

所以，假设我对每对基因只有一个分数。我的数据可以被视为无向图： alt text

并回想一下每条边都有一个分数。

现在，我想做的是：

以交互方式可视化我的数据：能够单击基因节点并打开附加到它们的链接，仅显示高于/低于某个阈值的边缘，控制网络如何“传播”等。
将组聚集在一起 是相似的，即具有相似的基因。

我该怎么做有什么想法吗？我想这是基本的集群，我希望任何有关软件包/软件的提示可以在这里提供任何帮助。

谢谢。

原文

I'm working with biological data - namely groups of genes. For example:

group 1: geneA geneB geneC
group 2: geneD geneE
group 3: geneF geneG geneH

For each pair of genes, geneX and geneY I have a score telling how similiar the two genes are (actually, I have two scores, since I used BLAST which is 'directional': I first searched geneX against all the other genes then geneY against all the other genes, so I have two geneX--geneY scores, but I guess I can take the lower score of the two, or the average).

So, let's suppose I have only one score for each pair of genes. My data can be viewed as a undirected graph:
alt text

and recall each edge has a score attached to it.

Now, what I would like to do is:

Visualize my data interactively: being able to click on gene nodes
and open a link attached to them, show only edges above/below some threshold, control how the network is "spread", etc.
Cluster together groups which
are similar, i.e. groups that have
similar genes.

Any ideas of how can I do that? I guess it's basic clustering and I would appreciate any hints on packages/software that can be of any help here.

Thank you.

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